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The layer selector divides residues into core, boundary, and surface regions based either on number of sidechain neighbors (the default) or solvent-accessible surface area, and then selects residues in one or more of these regions.

References and author information for the Layer residue selector:

LayerSelector ResidueSelector's citation(s): *Dang B, *Wu H, *Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva D-A, Baker D, and DeGrado WF. (2017). De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proc Natl Acad Sci USA 114(41):10852–10857. doi: 10.1073/pnas.1710695114. (*Co-primary authors.)

<Layer name="(&string;)" select_core="(false &bool;)"
        select_boundary="(false &bool;)" select_surface="(false &bool;)"
        cache_selection="(false &bool;)" use_sidechain_neighbors="(true &bool;)"
        asu_only="(false &bool;)" ball_radius="(&real;)"
        sc_neighbor_dist_midpoint="(&real;)" sc_neighbor_denominator="(&real;)"
        sc_neighbor_angle_shift_factor="(&real;)"
        sc_neighbor_angle_exponent="(&real;)"
        sc_neighbor_dist_exponent="(&real;)" core_cutoff="(&real;)"
        surface_cutoff="(&real;)" />
  • select_core: Should the core (buried) layer be selected?
  • select_boundary: Should the boundary (semi-buried) layer be selected?
  • select_surface: Should the surface (exposed) layer be selected?
  • cache_selection: Should the selection be stored, so that it needn't be recomputed?
  • use_sidechain_neighbors: If true (the default), then the sidechain neighbor algorithm is used to determine burial. If false, burial is based on SASA (solvent-accessible surface area) calculations.
  • asu_only: if true, returns selection of only asymmetric unit.
  • ball_radius: The radius value for the rolling ball algorithm used for SASA (solvent-accessible surface area) calculations. Only used if use_sidechain_neighbors=false.
  • sc_neighbor_dist_midpoint: The midpoint of the distance-dependent sigmoidal falloff for the sidechain-neighbors algorithm. Only used if use_sidechain_neighbors=true.
  • sc_neighbor_denominator: A parameter affecting the selection of residues by the method of sidechain neighbors. This almost never needs to be changed from its default value of 1.0.
  • sc_neighbor_angle_shift_factor: A parameter affecting the angular falloff when selecting residues by the method of sidechain neighbors. This rarely needs to be changed from its default value of 0.5.
  • sc_neighbor_angle_exponent: The angle exponent when selecting residues by the method of sidechain neighbors. This determines how fuzzy the edges of the cones are. The default value is 2.0. See the code in core/select/util/SelectResiduesByLayer.hh for more details of the algorithm.
  • sc_neighbor_dist_exponent: The distance exponent when selecting residues by the method of sidechain neighbors. This determines how fuzzy the distance cutoff is. The default value is 1.0. See the code in core/select/util/SelectResiduesByLayer.hh for more details of the algorithm.
  • core_cutoff: The cutoff value for considering a position to be part of the core. If use_sidechain_neighbors is true (the default), then positions with MORE than this number of neighbors will be counted as core, and the default value is 5.2 neighbors. (Note that the fuzziness of sidechain cones allows for non-integer neighbor counts.) If use_sidechain_neighbors is false, then positions with LESS than this amount of solvent-exposed surface area will be counted as core, and the default is 20.0 A.
  • surface_cutoff: The cutoff value for considering a position to be part of the surface. If use_sidechain_neighbors is true (the default), then positions with FEWER than this number of neighbors will be counted as surface, and the default value is 2.0 neighbors. (Note that the fuzziness of sidechain cones allows for non-integer neighbor counts.) If use_sidechain_neighbors is false, then positions with MORE than this amount of solvent-exposed surface area will be counted as surface, and the default is 40.0 A.